Video Tip of the Week: ENCODE Data at UCSC (reminder)

This week’s tip of the week is a reminder: go and watch the ENCODE tutorial that is sponsored by the UCSC Genome Browser’s ENCODE team. There now just one week of free access left.

One week left for free access to the movie, slides, and exercises

For a number of years a team at the UCSC Genome Browser group was designated as the DCC, or Data Coordination Center, charged with wrangling and display of ENCODE data so that everyone could access it as soon as possible. We covered the early stages of this in a tutorial about the ENCODE Foundations.

As the project matured and more and more data flowed in, the DCC folks created new tracks and displays and new management tools to work with the data. We created a second tutorial to explain and explore that: ENCODE Data at UCSC.

Thousands of people have come and watched the set of “free” suites that we have. However, sometimes the grants come to an end and we no longer have the support to keep them available. So soon we’ll be taking them from the “free” page and putting them in the subscription side. The materials will still be available by individual purchase or by institutional subscription.

A recent paper (cited below) provides details on a number of the features that we explore in the tutorial. The data types and the display strategies are discussed. Access tools and distribution details are provided. If you have a look at that paper and watch the tutorial you’ll have a great grasp of how to interact with the ENCODE data in the UCSC Genome Browser.

But you still have a week! Go watch the video from the “launch tutorial” button. Download the slides and exercises.

We’ll be keeping an eye on the next steps for the ENCODE project and the transition to the new DCC. And we’ll update the materials when it’s needed.

Quick links:

ENCODE Foundations tutorial suite: www.openhelix.com/ENCODE

ENCODE Data at UCSC tutorial suite: www.openhelix.com/ENCODE2

ENCODE Project landing page: www.encodeproject.org

References:

Rosenbloom, K., Sloan, C., Malladi, V., Dreszer, T., Learned, K., Kirkup, V., Wong, M., Maddren, M., Fang, R., Heitner, S., Lee, B., Barber, G., Harte, R., Diekhans, M., Long, J., Wilder, S., Zweig, A., Karolchik, D., Kuhn, R., Haussler, D., & Kent, W. (2012). ENCODE Data in the UCSC Genome Browser: year 5 update Nucleic Acids Research, 41 (D1) DOI: 10.1093/nar/gks1172